A Computer Assisted Receptor Map in Approach to ...

A Computer Assisted Receptor Map in Approach to the Design of Anti-AIDS Transcriptase Agents Directed at &#Reverse Mark A. Fisher: Prem N.S.Yadav*, Janardan Yadav**, Swamy Laxminarayan**, David Kristol#, Mukund Mod&

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*Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, Academic Computing Services, UMDNJ, 185 South Orange Avenue,Newark, New Jersey, 07103, 'Biomedical Engineering Department, New Jersey Institute of Technology,University Heights, Newark, New Jersey 07102 1. Introduction

RT.The systematic search is a tool for the generation and compariroo of

Rcvenc T"criptUc(RT) is U! RNAdqendent DNA polymerise c h u of enzyme that U crucial for the replication of many vinusa that u u s e serious disuses. The clelective blockage of the functioning of this enzyme may be expected to interfere with viral rrpliution. A number of nucleoridc 4 o g i (such as U T , ddI. ddT. WT. etc.) have been successfully u t i t i as effective inhibiton directed at RT However, the emergence of viral strains which exhibit resimnce to these d o g s U well as cellular toxicity concerns have mandated the scarch for new and highly clelective inhibitors. With this goal in mind we have taken a "Pharmacophoric" approach to the identification of a subetaateribitor bincling site on HIV-1 KT. A phannacophore is Mined as the spatial arrangement of a set of atoms or groups in a ligand molecule while bound to a given receptor. The phumrrcophore's usefulneur is in the asgumption that a single one exists for a series of compounda binding at the "e receptor site. The muperposition of a seriu of subatrate andlor inhibitors along a pharmacophoric pattern provides M clayme excluded volirme, which mpresenu a minimum volum requirement for substratelinhibitors at the receptor binding site. The structure of HIV-I RT complexed with dsDNA templateprimer has been recently described at 7 A molution and is cumntly being extended to 3 A. The combination of crystallographic, pharmacophoric, and existing biochemical and genetic data m g d i the subetaate binding residues, will help to generate an accurate structure of the arbatrate bindihg donuin of HIV-1KT and aide u1 the evaluation of new aod specific RT inhibitors.

all the sterically allowed C O ~ ~ O K X M ~a~ compound OM cm smme via the rotation of flexible boob. From a pharnvcophoric point of view, there muat be at leaat one bioactivc confornvtion in each analog that presenu a set of atoms with a common three diwnaioml orientation with reupcot to each other in dl mloga. Thio represenfa the pharmacophoric pattern adopted by thew analogs when bound to a given receptor. The task is, thua, LO systemtically compare the C O ~ O K I M ~ ~ Oof M a number of active analogs and identify what atomic groups are capable Qf presenting common three dimensional orientations.

2. Hardware and Software Molecular modeling studies were conducted on an Personal Ma workstation from Silicon Graphics running under the UNM operating system. The SYBYL molecular modeling software version 5.5 from Tripos Associates, Inc. was used for the representation and manipulation of'the structures used in this study.

The systematic .search with the superconatminingoption and concomitant orientation mp(0MAP) generation was used to identify the hetemtom pairs (from base, sugar, and phosphorylation sites) that are capable of moving thmughout s common range of interatomic distances. An Orientation map provide8 a method of molecular comparison that's independent of a compounds overall structure; thus, providing s metric which can be urtd to r a t i o ~ l l ycompare the similarities between structurally diverse compounds. It's baaed upon a relative distance space in which the distances between potential phamcophoric groups are used as the coordinate system. Heterortom pa& wen: selected for analysis because they are capable of engaging in hydrogen b o n d q and electroStatic interactions at s protein's surface. We investigated 1111 hetemtom pa& syatematically, alone and in combinations, to determine which wert capable of moving throughout a common interatomic distance qace(mee figure 1). An O W point is the actual interatomic distance values and is the aurrch data used to compare the confornvtioor of each test compound. A rcarch and ccmtrain methodology waa used to identify the hetemtom

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3. Procedure 3.1 Startinn Geometry

structures we= available for 3'-.zido-2',3'didmxyhymidm(AZT), 2'.3'didcoxythymidinc (ddT), and 3 ' 4 d o 2',3'didcoxyuridme(AzddU). We modified the cryrtal structure of ddT to make 2',3'didehyddideoxythymidine@4T). The inherent molecular distohons that occur during the formation of a c r y d structure necessitate the performance of a geometrical optimization of the starting struictures in MYmolecular modeling study. This will alleviate sterically bad contacts that may be present in some structures. Each structure was optimized by MAXMIN2 using the Tripos force field. Cryd

3.2 Pharmacouhore Identification: The Systematic Conformational

Starch In h i s presentation, we used the systematic search to suggest potential pharmacophores for thymidine nucleoside analog inhibiton of HIV-1

Q7803-0925-1193S03.00 01993 IEFE

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Figure 1:Heteroatom pairs.

We selected the lowest energy conformation of a c h compotd U pain with common ranges of motion in all our test compounds. This biorctive and used thew mctures for the generation of M excluded involves the generation of search data (OMAP points) for a volume map. Each biollctive conformation was superimposed dong the unconstrained lead compound in d of ita rtericdy dowed ptunuacophoric p u p s (02,04',and 0 5 ' ) and M enzyme excluded conformatiom. The next compound lurched would have the a r c h data volume was generated. This is the union volume of the superimpooed of the previous compound used to constrain the heteroatom pair motion active analogs and rcprerenta the minimum volume requirement at the in ita druchlre; resulting in the generation of c o n f o r m ~ t i owith ~ receptor site ( sec figure 3). heteroatom pair ~ r i e n t a t icommon ~~ to them both. In subsequently arched compounds, the lurch data of the dtucture lurched 4. Concluding Remarks immediately prior to itself will result in C O ~ O ~ ~ ~ ~having ~ O I I S In this p r e l i r y mdy, we identified the 0 2 , 0 4 ' , and 0 5 ' atoms U a heteroatom pair orientatiom common to it and d previoudy rurched potential pharmacophore for thymidine nucleoside d o g s targeted at compounds. With this approach, the MI compound searched will have RT. The validity of s pharmacophore predicted via thin approach is a set heteroatom pair orientations that uc common to d the compounds fu&er substantiated by ita application to a large number of active under investigation, if any (sec figure 2). The OMAP pointr auociated analogs and their ability to conform to it. Cumntly, we are e x p d h g with this compound will be used to constrain the searching of d k a t upon the information obtained in this study by includhg a number of compounds using the normal comtmhing option; and will remilt in all additional active d o g rtruchlrea and a modified a r c h criteria. We the conformation in each active d o g that is upable of adopting the seck to utilize the ayrtematic confonuational a r c h to fully investigate iven hetemtom orientation aanociated with the common OMAP pointa other p0tcnti.l pharmacophores. In the cumnt study, sugar puckering variatiom along with glycosidic and exocyclic hydroxyl bond rotation will be included as scarch variables.

5. Acknowledgments 9

We would like to extend our thanks to Dr. Leslie Michelaon for the use of the molecular modeling facilities at the University of Medicine and Dentistry of New Jersey.

6. References 1. Arnold, E.,"Smrctltreof HN-1 Reverse TranscriptaseLDhU Compla at 7 6 Showing Acdve Site Location", Nature. vol. 357, pp. 85-

Figure 2: Constmint example. Initially, searches involving single atom pairs were pcrformcd to identify the minimum level of ~ ~ " ~ n a lini each t y compound. This resulted in a number of OMAP pointa for each heteroatom pair that all the compounds under investigation we; capable of presenting. Subsequently, these pain were used in ~ ~ m b itot identify i ~ ~the maximum number heteroatom pain the test compounds could present with common orientatio~.Thir maximum number of heteroatom pairs and the OMAP pointa associated with them will serve U a tentative phannacophore. ' h e multiple paired searches resulted in the identification of pain C and E U the only pain in which d the test compounds had a common OMAP point. The atoms involved in these pairs are 02, 04'.and 0 5 ' . These heteroatom and the associated OMAP pointa have been proposed as a initialphamracophore.

89, 1992. 2. Amold, E.,unpublished data 3. Marshall, G.R., "CompmrAidcd Dmg Design", Annual Review of Phann. &Toxic., vol. 27, pp. 193-213, 1987 4. Yadav, J., Yadav, P.,Laxminarayan, S., Michelaon, L, Arnold, E., M d k , M.,'Computer Assisud Design of Antiviral Agents Dincud Against Rev." Transcriptuse as W r Target", of New York Academy of Sciences, vol. 616, pp. 624-630, 1991.

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The application of this OMAP point ( pairs C and E with rangcll of motion: 7.33 to 7.44 and 3.64 to 3.66 A, respectively) to each test compound resulted in the a number of conformations in each compound that were capable of presenting the given heteroatom orientations(sec table 1). Table 1: Conformatiom with common OMAP point. Comoound Conformatiom Am 144 ddT 36 3'-FddT 36 AzddU 144 D4T 36

Figure 3: Enzyme excluded volume map.